PLUS she will be in S3.
Evidence 1: There was an alternative option in which you can leave AJ, but it was erased. My theory is that the creators didn't want to make SO MANY ends (that would be 10 endings, right?), because that would mean 5, at least, diferent storylines. So they put the baby in all of them, so they just had to make 5 different beginnings and small variables in the story ("I gotta find my friend Kenny"; "I have to find my friend Jane", "I need to find my little brother" [because "I need to find my baby" would be like "You got a fucking baby?"]), idk, stuff, thaaaangs like that. (And why did they erase this option, if they are not going to be important characters? They just would have to do 5 edings more, with little variants, right? What bothered to them let us leave AJ behind? S3 STORYLINES!)
Evidence 2: In this video, this guy, Greg Miller (doesn't he appear in the credits in the game?) says he let Kenny kill Jane and then killed him "Because he wanted Clementine to be alone since the first episode in S3". Shouln't the people that works in TellTale know what the S3 in going to be about?
Evidence 3: In this same video, they started talking about how S1 and S2 were so different. And THEN they started to talk about S3 and its stupid New Angle. They said it was "going to be different". That doesn't really mean that Clementine won't be the protagonist. Actually, if Clem appears in S3, that directly means that she will be the protagonist. Beacuse her personality depends of the player's choices. They can't just make an scene with her, not being the protagonist, and don't make it seem weird. So she will be the protagonist or she won't be.
sorry for bad english.